This document is for an old release of Galaxy. You can alternatively view this page in the latest release if it exists or view the top of the latest release's documentation.

Source code for galaxy.util.compression_utils

import gzip
import io
import logging
import os
import tarfile
import zipfile

from galaxy.util.path import safe_relpath
from .checkers import (

log = logging.getLogger(__name__)

[docs]def get_fileobj(filename, mode="r", compressed_formats=None): """ Returns a fileobj. If the file is compressed, return an appropriate file reader. In text mode, always use 'utf-8' encoding. :param filename: path to file that should be opened :param mode: mode to pass to opener :param compressed_formats: list of allowed compressed file formats among 'bz2', 'gzip' and 'zip'. If left to None, all 3 formats are allowed """ return get_fileobj_raw(filename, mode, compressed_formats)[1]
[docs]def get_fileobj_raw(filename, mode="r", compressed_formats=None): if compressed_formats is None: compressed_formats = ['bz2', 'gzip', 'zip'] # Remove 't' from mode, which may cause an error for compressed files mode = mode.replace('t', '') # 'U' mode is deprecated, we open in 'r'. if mode == 'U': mode = 'r' compressed_format = None if 'gzip' in compressed_formats and is_gzip(filename): fh = gzip.GzipFile(filename, mode) compressed_format = 'gzip' elif 'bz2' in compressed_formats and is_bz2(filename): fh = bz2.BZ2File(filename, mode) compressed_format = 'bz2' elif 'zip' in compressed_formats and zipfile.is_zipfile(filename): # Return fileobj for the first file in a zip file. # 'b' is not allowed in the ZipFile mode argument # since it always opens files in binary mode. # For emulating text mode, we will be returning the binary fh in a # TextIOWrapper. zf_mode = mode.replace('b', '') with zipfile.ZipFile(filename, zf_mode) as zh: fh = zh.open(zh.namelist()[0], zf_mode) compressed_format = 'zip' elif 'b' in mode: return compressed_format, open(filename, mode) else: return compressed_format, open(filename, mode, encoding='utf-8') if 'b' not in mode: return compressed_format, io.TextIOWrapper(fh, encoding='utf-8') else: return compressed_format, fh
[docs]def file_iter(fname, sep=None): """ This generator iterates over a file and yields its lines splitted via the C{sep} parameter. Skips empty lines and lines starting with the C{#} character. >>> lines = [ line for line in file_iter(__file__) ] >>> len(lines) != 0 True """ with get_fileobj(fname) as fh: for line in fh: if line and line[0] != '#': yield line.split(sep)
[docs]class CompressedFile:
[docs] @staticmethod def can_decompress(file_path): return tarfile.is_tarfile(file_path) or zipfile.is_zipfile(file_path)
[docs] def __init__(self, file_path, mode='r'): if tarfile.is_tarfile(file_path): self.file_type = 'tar' elif zipfile.is_zipfile(file_path) and not file_path.endswith('.jar'): self.file_type = 'zip' self.file_name = os.path.splitext(os.path.basename(file_path))[0] if self.file_name.endswith('.tar'): self.file_name = os.path.splitext(self.file_name)[0] self.type = self.file_type method = 'open_%s' % self.file_type if hasattr(self, method): self.archive = getattr(self, method)(file_path, mode) else: raise NameError('File type %s specified, no open method found.' % self.file_type)
@property def common_prefix_dir(self): """ Get the common prefix directory for all the files in the archive, if any. Returns '' if the archive contains multiple files and/or directories at the root of the archive. """ contents = self.getmembers() common_prefix = '' if len(contents) > 1: common_prefix = os.path.commonprefix([self.getname(item) for item in contents]) # If the common_prefix does not end with a slash, check that is a # directory and all other files are contained in it if len(common_prefix) >= 1 and not common_prefix.endswith(os.sep) and self.isdir(self.getmember(common_prefix)) \ and all(self.getname(item).startswith(common_prefix + os.sep) for item in contents if self.isfile(item)): common_prefix += os.sep if not common_prefix.endswith(os.sep): common_prefix = '' return common_prefix
[docs] def extract(self, path): '''Determine the path to which the archive should be extracted.''' contents = self.getmembers() extraction_path = path common_prefix_dir = self.common_prefix_dir if len(contents) == 1: # The archive contains a single file, return the extraction path. if self.isfile(contents[0]): extraction_path = os.path.join(path, self.file_name) if not os.path.exists(extraction_path): os.makedirs(extraction_path) self.archive.extractall(extraction_path, members=self.safemembers()) else: if not common_prefix_dir: extraction_path = os.path.join(path, self.file_name) if not os.path.exists(extraction_path): os.makedirs(extraction_path) self.archive.extractall(extraction_path, members=self.safemembers()) # Since .zip files store unix permissions separately, we need to iterate through the zip file # and set permissions on extracted members. if self.file_type == 'zip': for zipped_file in contents: filename = self.getname(zipped_file) absolute_filepath = os.path.join(extraction_path, filename) external_attributes = self.archive.getinfo(filename).external_attr # The 2 least significant bytes are irrelevant, the next two contain unix permissions. unix_permissions = external_attributes >> 16 if unix_permissions != 0: if os.path.exists(absolute_filepath): os.chmod(absolute_filepath, unix_permissions) else: log.warning("Unable to change permission on extracted file '%s' as it does not exist" % absolute_filepath) return os.path.abspath(os.path.join(extraction_path, common_prefix_dir))
[docs] def safemembers(self): members = self.archive common_prefix_dir = self.common_prefix_dir if self.file_type == "tar": for finfo in members: if not safe_relpath(finfo.name): raise Exception("Path '%s' is blocked (illegal path)." % finfo.name) if finfo.issym() or finfo.islnk(): link_target = os.path.join(os.path.dirname(finfo.name), finfo.linkname) if not safe_relpath(link_target) or not os.path.normpath(link_target).startswith(common_prefix_dir): raise Exception(f"Link '{finfo.name}' to '{finfo.linkname}' is blocked.") yield finfo elif self.file_type == "zip": for name in members.namelist(): if not safe_relpath(name): raise Exception(name + " is blocked (illegal path).") yield name
[docs] def getmembers_tar(self): return self.archive.getmembers()
[docs] def getmembers_zip(self): return self.archive.infolist()
[docs] def getname_tar(self, item): return item.name
[docs] def getname_zip(self, item): return item.filename
[docs] def getmember(self, name): for member in self.getmembers(): if self.getname(member) == name: return member
[docs] def getmembers(self): return getattr(self, 'getmembers_%s' % self.type)()
[docs] def getname(self, member): return getattr(self, 'getname_%s' % self.type)(member)
[docs] def isdir(self, member): return getattr(self, 'isdir_%s' % self.type)(member)
[docs] def isdir_tar(self, member): return member.isdir()
[docs] def isdir_zip(self, member): if member.filename.endswith(os.sep): return True return False
[docs] def isfile(self, member): if not self.isdir(member): return True return False
[docs] def open_tar(self, filepath, mode): return tarfile.open(filepath, mode, errorlevel=0)
[docs] def open_zip(self, filepath, mode): return zipfile.ZipFile(filepath, mode)
[docs] def zipfile_ok(self, path_to_archive): """ This function is a bit pedantic and not functionally necessary. It checks whether there is no file pointing outside of the extraction, because ZipFile.extractall() has some potential security holes. See python zipfile documentation for more details. """ basename = os.path.realpath(os.path.dirname(path_to_archive)) zip_archive = zipfile.ZipFile(path_to_archive) for member in zip_archive.namelist(): member_path = os.path.realpath(os.path.join(basename, member)) if not member_path.startswith(basename): return False return True